chr2-240573117-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018226.6(RNPEPL1):c.677C>T(p.Ser226Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000157 in 1,605,322 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018226.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNPEPL1 | NM_018226.6 | c.677C>T | p.Ser226Leu | missense_variant | 3/11 | ENST00000270357.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNPEPL1 | ENST00000270357.10 | c.677C>T | p.Ser226Leu | missense_variant | 3/11 | 1 | NM_018226.6 | P1 | |
RNPEPL1 | ENST00000451363.5 | c.-56-1398C>T | intron_variant | 4 | |||||
RNPEPL1 | ENST00000486058.5 | n.403C>T | non_coding_transcript_exon_variant | 3/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152170Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000159 AC: 38AN: 238256Hom.: 0 AF XY: 0.000186 AC XY: 24AN XY: 129298
GnomAD4 exome AF: 0.000156 AC: 226AN: 1453034Hom.: 0 Cov.: 33 AF XY: 0.000190 AC XY: 137AN XY: 721886
GnomAD4 genome AF: 0.000171 AC: 26AN: 152288Hom.: 0 Cov.: 34 AF XY: 0.000148 AC XY: 11AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.677C>T (p.S226L) alteration is located in exon 3 (coding exon 3) of the RNPEPL1 gene. This alteration results from a C to T substitution at nucleotide position 677, causing the serine (S) at amino acid position 226 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at